annotate select_product.xml @ 5:738310b31de0 draft

Uploaded
author brigidar
date Thu, 08 Oct 2015 22:48:23 -0400
parents f2506dfbc7f7
children 8eb1751dcfe7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
f2506dfbc7f7 Uploaded
brigidar
parents: 3
diff changeset
1 <tool id="select_product" name="select_product" version="0.3">
3
342d303e5468 Uploaded
brigidar
parents: 2
diff changeset
2 <description>define product names to sort on and flanking region</description>
1
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
3 <requirements>
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
4
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
5 </requirements>
4
f2506dfbc7f7 Uploaded
brigidar
parents: 3
diff changeset
6 <command interpreter="python">
1
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
7 select_product.py
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
8 -g $input_file
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
9 -n $number
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
10 -k $keys
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
11 > output_file
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
12 </command>
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
13
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
14 <inputs>
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
15 <param format="gbk" name="input_file" type="data" label="reference genbank file"/>
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
16 <param name="number" type="integer" value="50" label="flanking region"/>
3
342d303e5468 Uploaded
brigidar
parents: 2
diff changeset
17 <param name="keys" type="text" label=" list of keys separated by comma of product names"/>
1
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
18 </inputs>
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
19
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
20
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
21 <outputs>
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
22 <data format="tabular" name="output_file" from_work_dir="output_file">
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
23 </data>
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
24
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
25
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
26 </outputs>
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
27
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
28 <tests>
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
29 <!-- Empty -->
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
30 </tests>
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
31
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
32 <help>
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
33
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
34 .. class:: infomark
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
35
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
36 **What it does**
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
37
3
342d303e5468 Uploaded
brigidar
parents: 2
diff changeset
38
342d303e5468 Uploaded
brigidar
parents: 2
diff changeset
39 Finds all CDS that match the key words provided in the comma separated argument -k in the product description adds a given number of bases on each side of the transcript for the exclusion set
342d303e5468 Uploaded
brigidar
parents: 2
diff changeset
40
2
04128b8f7bc7 Uploaded
brigidar
parents: 1
diff changeset
41
1
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
42 -------------
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
43
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
44 .. class:: infomark
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
45
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
46 **Tool Author**
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
47
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
48 Brigida Rusconi
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
49
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
50
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
51 </help>
c76d2a6bedee Uploaded
brigidar
parents:
diff changeset
52 </tool>